A late betrayal
by Love me hate me 29
Summary: The Third Hokage dosen't find Orochimaru that night experimenting on people just an ordinary doctor. Orochimaru's off the hook and he has a reason to stay because he just discovered something not natural. R&R


**A/N: This is a new story whose idea just struck me while I was on a flight. Uploaded the improved version of the Unexpected advice as promised when I removed the story before.**

**Please read and review because I still need to improve a lot and your reviews just make my day.**

Midnight was slowly approaching unknown to the elder man sitting in his office engaged in his work. Paper after paper was read and stamped or rejected. He scoffed on reading some of them, chuckled at some and some of them were carefully read and marked for further review. His office was heavily guarded by ninjas hidden in the shadows. He was aware of all of them even the one that was hidden under Genjutsus. This man was most probably the strongest man in his village and it was a pity to see him reduced to this state.

This man was the Sandaime Hokage of Konoha.

The Sandaime took a deep breath after completing one of the piles of the mountains of paperwork around him and lit up his pipe for a smoke. Letting out a huge sigh he decided to call it a night. As he slowly stood up he winced as the old bones creaked and pain erupted in his knees. He sighed again and started walking towards the exit.

"Go home Inu, you just came from a mission in the morning and reported straight back to duty. Please go and rest and don't report back until tomorrow evening." He said while walking away.

Things had gone from bad to worse after the Kyuubi's attack. The death of Namikaze Minato had affected the life of every Konohan inhabitant directly or indirectly. Some were hit quite harder than everyone else. Kakashi, Minato's student had returned back to his former shell, becoming cold and indifferent towards everyone. Hiashi, the Hyuuga clan head and former teammate of the Namikaze had immersed himself into his clan duties and had become even more colder than before and the death of his wife had worsened the situation further. Rin, Minato's other student had disappeared and no trails were found which also affected Kakashi who believed that he was unable to save another of his teammate.

Also the loss of hundreds of Shinobi was a big blow to Konoha's force and it was now no longer as strong as before. His paperwork had increased so much in the last 4 years that he rarely had any time outside his office and he had not seen his students or Naruto for atleast a year. Tsunade and Jiraiya were long gone unable to hold the pain anymore. Although Jiraiya seldom reported back to him through his toad summons but it was not as good as seeing him face to face. The aging leader longed to see his old team together with all his children like students. Jiraiya's goofy smile, Tsunade's furious face when Jiraiya called her flat-chested and last but not the least Orochimaru's eyes lighting up in innocent wonder whenever he saw a new application of chakra or a new jutsu.

After the Kyuubi's attack people had started disappearing and all the clues had pointed towards his student Orochimaru. With a heavy heart he had gone to confront him only to find another person who was then the head of the hospital performing experiments on civilians there. Confused he believed that the most probable answer was that his student was being framed. Soon after that the disappearances stopped and Orochimaru was laid of the hook but something in Sandaime still refused to believe that his student was innocent.

His timely disappearances, no alibis, the nonchalant attitude towards the kidnapping were alarming signs but he still couldn't bring himself to confront his son-like student. But after four years the Sandaime believed that Orochimaru had definitely changed. Although he didn't interact with anyone, he still had a apprentice of 6 years Anko Mitarashi and had helped in maintaining a strong image of Konoha in front of their rival countries by being the only Sannin still present in Konoha.

'All's well that ends well' was the Sandaime's last thought as he left the Hokage's Tower.

On the other side of Konoha 10 feet under the ground the Snake Sannin was preparing for his latest experiment.

**-xx- **

Orochimaru sat down heavily in his chair exhausted. His eyes roamed around his main laboratory taking in all the successes and the failures. This was his main laboratory situated deep below Konoha. Being an old 'Ne' base it had no official records and he had immediately seized the opportunity. Finally his eyes came back to what laid in front of him. It was maybe his biggest achievement since his immortality jutsu and it had taken him straight 4 years to complete what he had started. Four years ago he had heard about the Akatsuki organization and its members and about the rumors circulating about the legendary doujutsu 'Rinnegan' emerging in the ruins of Amegakure. He had known about the student possessing the Rinnegan that Jiraiya had and had cursed the fool for losing an opportunity of a millennium by letting the child die but now he knew that maybe Jiraiya's information was wrong. So he had decided to let go of caution and to complete as many of his experiments as possible before he left the village.

One day as he was planning his escape path with the help of multiples snake summons one of them stumbled upon something that could only be called a big lump of shining rock. Excited that maybe he had found a meteor like the one present in the Hidden Star village he quickly took it to his lab. He had seen the meteor in Hidden Star village before and had also studied a sample illegally but he never got his hands on such a big sample. Wearing all protective measures as the meteor previously discovered was known to be quite radioactive he started the preliminary inspection only to find that the substance in front of him was no meteor but quite a complex ore of a metal he had never seen before. Interested he continued his inspection. After 3 days and 3 sleepless nights of continuous experimenting and extraction to say that he was amazed would have been an understatement.

The substance responded to chakra. Chakra instructed it to store, it stored, it told it shape itself into something, and it did it. If chakra told it to destruct, well then the explosions were one of the biggest Orochimaru had ever seen.

The metal hence extracted quite difficultly I might add was a 100% charka conductive substance. Not an ounce of chakra was lost during its channeling through the metal. Hell even 20% of the chakra was lost or absorbed when it was channeled through the body from the respective chakra gates as heat or light. Seals engraved on the metal operated at full efficiency. Chakra transport seals which previously were the least efficient ones and only transported about one-tenths of chakra were now used almost daily by him and had very comfortably settled into his designs of the Curse seal of Heaven. He had then summoned hundreds of snakes and had let them scout the area for more of the ore and surprisingly he had found more, a lot more.

He was in Konoha so he could fully use all his resources on uncovering the secrets the metal held. He needed the security provided by the village as long as he had the project going on. Replacing himself with Dr. Yakushi he had averted the suspicion off himself. It had taken him full four years to finally discover the extent of the uses the metal offered. After four years, he was again ready to leave the village equipped with weapons made by the metal he now called the CSC (Chakra Super Conductor). The ores were depleted. But he had just enough left for a last experiment.

**-xx- **

Naruto, aged 4 was wandering in the streets as the clock approached midnight. The matron had thrown him out of the orphanage complaining about him bringing snakes into the building. He had already been asleep when the snakes had come and he had no idea how and who bought them inside. Still like always he was the first one to be blamed for everything that happened in the orphanage. He was blamed for the broken windows, stolen food (if he had really stolen the amount of food they said he did he would have been quite round not the malnutritioned moving skeleton.) and the previous matron had even blamed him for her husband leaving her. Slowly he walked through the streets careful of every shadow and corner with no destination in his mind. He was feeling sleepy. Shaking himself he scouted around for a place to sleep and found a park nearby. Settling himself on the bench he tried fanning himself with his hands. It was a hot summer night. The kind of night when you lay down to sleep you keep waking up at different intervals at night just due to the heat.

**-xx-**

Naruto woke up due to the heat after a hour and tried to shift his position. Unable to sleep he opened his eyes and saw the stars shining brightly in the night sky. There was no moon in the sky. Little Naruto had always wondered why the moon hid itself on some days. He had tried to ask a few people only to get ignored. Finally he had given up.

He watched the stars, trying to count them but always forgetting the digits after ten. One of the stars was shining brightly.

"Is that you mom? Jiji told me you died after you left. Can you see me from up there" asked Naruto softly.

"I miss you mom. But jiji told me that you wanted me to be strong, just like you were. But still mom I miss you so much." He continued unable to stop the tears. Wiping them quickly he took a quick survey around to see if anybody had seen him. Finding just the empty park he looked up again to see the clouds starting to cover the stars. Desperately trying to find the star again but without success Naruto finally gave up and went into sleep.

**-xx-**

This time Naruto woke up again expecting to find the sky again but instead found himself staring right into the surgical lights. Wincing, he closed his eyes tightly and then slightly opened them for them to get adjusted to the bright light. He tried to move himself only for the straps to restrict him. Panicking, he used more force but to no avail. Trying to calm himself as he felt tears picking his eyes, Naruto surveyed the room. It was a medium sized 15X15 feet room with some weird machines kept at the corners. Only the table to which he was bound was lighted. The rest of the room was dark. Different sharp objects ranging from scalpels to butcher knives decorated the tables around him. Looking away from the lights he let his eyes adjust to the dark and he was able to make out a figure leaning on the wall opposite to the table he lay on.

"Hey! Please untie me." Naruto called.

"Hello! Please lady. Untie me." Naruto was able to make out a feminine body.

"Miss. Why am I tied? I really didn't let those snakes in the orphanage. I swear" Naruto asked once again this time with more desperation in his voice. Hearing that, the person flinched. Not that Naruto could make it out from so far.

Unable to stop his tears now, Naruto quietly wept and laid still quietly.

"You know? I didn't do any of those things those guys say I did. I am a good boy. I even say the prayer that the old matron told me to. Daily. She told me it will help me repent for my bad doings. But when I asked what I did wrong she beat me. I really didn't do anything. Don't beat me." He just whispered.

There had been a reason that the matron had been removed. ANBU always kept a watch on Naruto in shifts. There was even an emergency tracking seal on the boy. But the Anbu who had kept watch today was still in the tree he was keeping a watch from with his neck bent quite oddly and his warm body still cooling.

**-xx-**

Everything was quiet for a while except for the barely heard beeping of the machines and the occasional sobs from Naruto.

Then there was the sound of the door opening. Both the feminine figure and Naruto turned their heads towards the newcomer. Naruto watched as the lady bowed to the man in front of her.

"Aaah! So my young apprentice you bought the boy for my final experiment? Excellent!" He paused. "Why you are crying?" the shrill voice said.

"Nothing, the formalin is just causing some irritation in my eyes. The boy is already on the table." The other replied.

"Well, that's good." Saying this he went forward into the brighter part of the room.

Naruto flinched on seeing the snake like man.

"Who are you and what are you going to do to me?" He asked trying to put up a brave face but failing miserably.

Orochimaru grinned on seeing this.

"Oh! What a brave boy you are Naruto-kun." He paused to see confusion on Naruto's face then recognition. "So, you remember me?"

"You are one of jiji's students." He remembered once meeting the guy when he visited the Hokage. 'He is one of Jiji's students so he must be a nice guy and wouldn't hurt me' thought Naruto.

"That's correct. Now, we must continue with our schedule. Schedule is important. Isn't that right Naruto-kun?" Orochimaru said as he moved the machines near to the operating table.

Naruto remembered that the Hokage had once told him that the schedule is very important and hence he couldn't stay longer for his monthly visit. That was atleast a year ago.

"Yes, Jiji told me that schedule is important. Now if you can please untie me it is getting very uncomfortable." Naruto said. In real he wanted to wipe his tears. Everybody laughed when he cried and this time he didn't want the Hokage's student to laugh at him!

"That would not be possible Naruto-kun. Here hold this between your teeth." He said giving Naruto a thick cloth.

"But, sensei what about the anesthesia? The boy will die of pain!" the girl shouted in near hysterics. Naruto observed that the feminine figure he had seen was this girl. She looked like 13 or 14 years old. Naruto had learnt to determine the age of children simply by looking at them so as to know which ones to avoid and which not.

"Anko! Keep quiet. Anesthesia won't work on him due to Kyuubi's chakra. We have to continue the experiment without it and you" He said pointing a glare towards the little boy. "put it in your mouth."

Now Naruto was seriously scared and did what he was told. He watched as Orochimaru put more straps around his chest and knees. He tried to shout in terror when he saw the man taking out long drills out the machines but as soon as he opened his mouth it was taped with the cloth still inside. Each second was a horror as the man in front of him placed the drills near his body.

'Jiji will come and save me. Like always. He will come.' The hokage had always came or sent his people to save him whenever he was in trouble and although he was not sure of it this time he still kept hope.

**-xx-**

Orochimaru was getting seriously annoyed. Why can't I get some good assistant? Anko was getting too emotional. That Kabuto boy looks promising.

Also, he was unable to remove the tracking seal from the boy.

'Definitely the work of my old stupid teammate.' He thought.

'As soon as Naruto would be in pain the seal would activate sending signal directly to the Anbu headquarters where a squad of atleast 20 members would be dispatched in an interval of 2 minutes. Make it 5 minutes because of the dead Anbu on the other side of Konoha. Another 10 to find the route to his laboratory and another 15 to beat his traps and reach him. So he had 25 minutes to complete his experiment and 5 to escape and leave his apprentice behind.'

His experiment was to determine whether the CSC was capable of being placed in a body having more than normal regeneration so as to increase the charka channeling speed and to decrease the lose of chakra being channeled mainly when the chakra gates were opened. Only about one-hundred of the amount of chakra released on opening the gates was usable the rest was lost. The death due to opening the 8th gate was solely due to the excess chakra that tore away the body and the body in the effort to confine the chakra into the pathways gets tired and hence the heart stops. Being able to use the full amount of chakra offered by the gates without the side effects was a miracle which if his calculations were correct including the first hokage's notes about the regeneration powers of the Kyuubi jinchuuriki his experiment was going to happen.

As soon as success was achieved he would kill the boy and if it was a failure then the boy's chakra pathways would be destroyed making him unable to be a shinobi. Both would be good for the start of his revenge against his sensei and if DNA results were to be believed a revenge against his long dead hokage contender.

**-xx-**

Naruto was in a world of pain. He wanted to close his eyes and go to sleep, maybe forever but now he wanted to sleep. 'Mom I am coming to you'. But he just couldn't faint. No matter how much he tried.

Orochimaru had inserted drills in all the major tenketsu was now guiding the CSC with his chakra to spread all over the body's chakra pathways. The Kyuubi's chakra was trying to reject the foreign matter from the body. Orochimaru was sweating bullets till the halfway completion. He had pumped Adrenaline in the boy's body so that he encountered least resistance due to increased bodily functions but it had hardly helped except by keeping the boy conscious.

Suddenly the pressure was released and Orochimaru was able to guide ithe CSC very easily. He narrowed his eyes there was no resistance, not even the natural one that was offered by the body.

Just as suddenly as the pressure had left, negative pressure skyrocketed. The CSC was sucked from the machines into the body. Red chakra lighted up the room. It controlled the CSC as easily as a river flowed. The metal formed different shapes. It broke things around in the lab, made high chakra bursts and it did one thing that Orochimaru had forgotten to consider even when it was right before his face- it regenerated, it multipled as the Kyuubi's chakra order it to do so. With the chakra there was an infinite amount of the metal available to the Kyuubi.

Orochimaru ran for the kill before the thing before him could become a threat only to dodge snakes that attacked him.

"Anko this is not the time!" He shouted still trying to reach the boy.

"You have killed enough innocent people. No more. I can't take even a single more on my conscience especially a child who has been abused all his life." She shouted.

She wanted to continue but was cutoff by a kick to the stomach and was thrown out of the room.

Orochimaru tried going near the boy to finish his job but it was too late. Anko's stupid actions had cost him the time.

He quickly went underground as the large chakra burst occurred and was even felt by the sensors in Suna.

Inside the 4 year old boy the huge chakra beast chuckled as it set to work on its host's body.

**-xx-**

The Sandaime sat beside the bed where Naruto laid. He slowly ran his hand to remove the hair falling on the boy's forehead.

Orochimaru's underground facility had become nothing more than ruins. The first to the scene had described the area as a metallic graveyard. Spikes originating from the table in which Naruto had been laid on had spread 100 metres in all directions and with time the farthest ones away from him faded away into just thin air progressing till there was nothing left for them to investigate. They had found a quite heavily injured Anko carrying an unconscious Naruto only to hand him before falling face first to the ground.

The doctors were still unable to reach to a conclusion about what was done to the boy. A metallic substance had hardened around the boy's chakra passages and had also spread to the bones covering them making them quite resilient. The substance wasn't toxic but it just disintegrated whenever they bought it out of the boy's body so nothing could be made out. His vitals were working fine and he was expected to wake up soon.

They would only be able to tell the extent of damage when Naruto woke up and that was not the only damage they had to consider. The mental scarring would change the boy. No medic present in Konoha was capable of curing the damage.

'Where are you Tsunade when we really need you?' Thought the old hokage who looked older with each passing day.

**A/N: Well that's a wrap. So, what do you think. Story worth continuing?**


End file.
